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- EMDB-73698: Composite cryo-EM density map of DNMT1 in complex with unmethylat... -

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Basic information

Entry
Database: EMDB / ID: EMD-73698
TitleComposite cryo-EM density map of DNMT1 in complex with unmethylated nucleosome core particle
Map data
Sample
  • Complex: WT DNMT1-umNCP complex
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • DNA: Chain x DNA (149-MER)
    • DNA: Chain Y DNA (149-MER)
  • Ligand: ZINC ION
KeywordsDNA C5 methyltransferase / Nucleosome complex / TRANSFERASE-DNA-DNA Binding Protein complex / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


histone H3K23ub reader activity / negative regulation of phenotypic switching / histone H3K18ub reader activity / histone H3K14ub reader activity / negative regulation of vascular associated smooth muscle cell differentiation / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity ...histone H3K23ub reader activity / negative regulation of phenotypic switching / histone H3K18ub reader activity / histone H3K14ub reader activity / negative regulation of vascular associated smooth muscle cell differentiation / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / STAT3 nuclear events downstream of ALK signaling / SUMOylation of DNA methylation proteins / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / lncRNA binding / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / heterochromatin / Nuclear events stimulated by ALK signaling in cancer / DNA methylation / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / promoter-specific chromatin binding / NoRC negatively regulates rRNA expression / nucleosomal DNA binding / innate immune response in mucosa / structural constituent of chromatin / nucleosome assembly / nucleosome / chromatin organization / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / antibacterial humoral response / protein heterodimerization activity / negative regulation of gene expression / chromosome / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / CXXC zinc finger domain / Zinc finger, CXXC-type ...DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / : / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / : / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone H3 / Histone H2B 1.1 / DNA (cytosine-5)-methyltransferase 1 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsFang J / Song J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119721 United States
CitationJournal: Nat Commun / Year: 2026
Title: The DNMT1 CXXC domain senses CpG islands for DNA methylation inhibition.
Authors: Jian Fang / Bo Pan / Wendan Ren / Jiuwei Lu / Ting Zhao / Yiran Guo / Ling Cai / Yinsheng Wang / Gang Greg Wang / Jikui Song /
Abstract: DNA methyltransferase DNMT1 plays an essential role in maintaining DNA methylation homeostasis. While DNMT1-mediated DNA methylation mainly occurs outside the active chromatin domains, such as CpG ...DNA methyltransferase DNMT1 plays an essential role in maintaining DNA methylation homeostasis. While DNMT1-mediated DNA methylation mainly occurs outside the active chromatin domains, such as CpG islands, how DNMT1 interplays with hypomethylated nucleosome environment to restrict CpG island methylation remains unclear. Here we report the structure of DNMT1 with a nucleosome containing unmodified CpG sites. The interaction of the DNMT1 CXXC domain with the unmodified CpG sites within the nucleosome core or the linker strengthens the DNMT1-nucleosome association, which contributes to the enrichment of DNMT1 in CpG islands. On the other hand, the CXXC domain is positioned in a manner that blocks the target recognition domain of DNMT1 from accessing potential DNA substrates. Consistently, disrupting the CXXC-CpG interaction leads to DNMT1 hyperactivity on nucleosomes with unmodified CpG sites, or those with spatially proximate unmodified and hemimethylated CpG sites. Furthermore, our whole-genome bisulfite-sequencing analysis reveals that introducing the CXXC-CpG interaction-defective DNMT1 mutation leads to substantial increase in CpG island methylation but not so much in overall genomic methylation, causing severe defects in transcriptional programming and stem cell differentiation. Together, this study establishes a role for the CXXC domain in safeguarding the CpG island hypomethylation, vital to DNA methylation homeostasis during development.
History
DepositionOct 31, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateNov 4, 2026-
Current statusNov 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73698.png

Downloads & links

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Map

FileDownload / File: emd_73698.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.8
Minimum - Maximum-11.618892000000001 - 45.68703
Average (Standard dev.)-0.0249688 (±0.7249492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : WT DNMT1-umNCP complex

EntireName: WT DNMT1-umNCP complex
Components
  • Complex: WT DNMT1-umNCP complex
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • DNA: Chain x DNA (149-MER)
    • DNA: Chain Y DNA (149-MER)
  • Ligand: ZINC ION

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Supramolecule #1: WT DNMT1-umNCP complex

SupramoleculeName: WT DNMT1-umNCP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA (cytosine-5)-methyltransferase 1

MacromoleculeName: DNA (cytosine-5)-methyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 141.358141 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: PKCIQCGQYL DDPDLKYGQH PPDAVDEPQM LTNEKLSIFD ANESGFESYE ALPQHKLTCF SVYCKHGHLC PIDTGLIEKN IELFFSGSA KPIYDDDPSL EGGVNGKNLG PINEWWITGF DGGEKALIGF STSFAEYILM DPSPEYAPIF GLMQEKIYIS K IVVEFLQS ...String:
PKCIQCGQYL DDPDLKYGQH PPDAVDEPQM LTNEKLSIFD ANESGFESYE ALPQHKLTCF SVYCKHGHLC PIDTGLIEKN IELFFSGSA KPIYDDDPSL EGGVNGKNLG PINEWWITGF DGGEKALIGF STSFAEYILM DPSPEYAPIF GLMQEKIYIS K IVVEFLQS NSDSTYEDLI NKIETTVPPS GLNLNRFTED SLLRHAQFVV EQVESYDEAG DSDEQPIFLT PCMRDLIKLA GV TLGQRRA QARRQTIRHS TREKDRGPTK ATTTKLVYQI FDTFFAEQIE KDDREDKENA FKRRRCGVCE VCQQPECGKC KAC KDMVKF GGSGRSKQAC QERRCPNMAM KEADDDEEVD DNIPEMPSPK KMHQGKKKKQ NKNRISWVGE AVKTDGKKSY YKKV CIDAE TLEVGDCVSV IPDDSSKPLY LARVTALWED SSNGQMFHAH WFCAGTDTVL GATSDPLELF LVDECEDMQL SYIHS KVKV IYKAPSENWA MEGGMDPESL LEGDDGKTYF YQLWYDQDYA RFESPPKTQP TEDNKFKFCV SCARLAEMRQ KEIPRV LEQ LEDLDSRVLY YSATKNGILY RVGDGVYLPP EAFTFNIKLS SPVKRPRKEP VDEDLYPEHY RKYSDYIKGS NLDAPEP YR IGRIKEIFCP KKSNGRPNET DIKIRVNKFY RPENTHKSTP ASYHADINLL YWSDEEAVVD FKAVQGRCTV EYGEDLPE C VQVYSMGGPN RFYFLEAYNA KSKSFEDPPN HARSPGNKGK GKGKGKGKPK SQACEPSEPE IEIKLPKLRT LDVFSGCGG LSEGFHQAGI SDTLWAIEMW DPAAQAFRLN NPGSTVFTED CNILLKLVMA GETTNSRGQR LPQKGDVEML CGGPPCQGFS GMNRFNSRT YSKFKNSLVV SFLSYCDYYR PRFFLLENVR NFVSFKRSMV LKLTLRCLVR MGYQCTFGVL QAGQYGVAQT R RRAIILAA APGEKLPLFP EPLHVFAPRA CQLSVVVDDK KFVSNITRLS SGPFRTITVR DTMSDLPEVR NGASALEISY NG EPQSWFQ RQLRGAQYQP ILRDHICKDM SALVAARMRH IPLAPGSDWR DLPNIEVRLS DGTMARKLRY THHDRKNGRS SSG ALRGVC SCVEAGKACD PAARQFNTLI PWCLPHTGNR HNHWAGLYGR LEWDGFFSTT VTNPEPMGKQ GRVLHPEQHR VVSV RECAR SQGFPDTYRL FGNILDKHRQ VGNAVPPPLA KAIGLEIKLC MLAKA

UniProtKB: DNA (cytosine-5)-methyltransferase 1

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Macromolecule #2: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A

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Macromolecule #3: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #4: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.366987 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARTKQTARK STGGKAPRCQ LATCAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LSAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.454546 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR (ML3)VLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEH AKR KTVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #6: Chain x DNA (149-MER)

MacromoleculeName: Chain x DNA (149-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 46.230461 KDa
SequenceString: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String:
(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA)(DG)(DA)(DA)

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Macromolecule #7: Chain Y DNA (149-MER)

MacromoleculeName: Chain Y DNA (149-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 45.754141 KDa
SequenceString: (DT)(DT)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA) (DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT) (DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG) (DT) (DA)(DG)(DA)(DC)(DA)(DG) ...String:
(DT)(DT)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA) (DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT) (DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG) (DT) (DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT) (DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC) (DT)(DT) (DA)(DA)(DA)(DC)(DG)(DC)(DA) (DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT) (DG)(DT)(DC) (DC)(DC)(DC)(DC)(DG)(DC) (DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG) (DC)(DC)(DA)(DA) (DG)(DG)(DG)(DG)(DA) (DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA) (DG)(DT)(DC)(DT)(DC) (DC)(DA)(DG)(DG) (DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG) (DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC)(DA) (DT)(DC)(DC)(DT)(DG)(DT)

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: ZN
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.13 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
50.0 mMNaClSodium chloride
5.0 mMDTTDithiothreitol
5.0 %GlycerolGlycerol
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 16915 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6950000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 212957
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial model
PDB IDChainDetails

7jzv

source_name: PDB, initial_model_type: experimental modelFor nucleosome

4wxx

chain_id: A, source_name: PDB, initial_model_type: experimental modelDNMT1

3pta

chain_id: A, source_name: PDB, initial_model_type: experimental modelDNMT1
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9z07:
Cryo-EM structure of DNMT1 in complex with unmethylated nucleosome core particle

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